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PubMed2002

The Protein Information Resource: an integrated public resource of functional annotation of proteins.

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).

Amino Acid Sequence↗

PubMed1998

A graphical WWW-database on gene expression in tooth.

We have constructed a WWW-site that presents gene expression in developing dental tissues (Gene expression in tooth, http://honeybee.helsinki.fi/toothexp). Our aim is to provide a tool for learning and for research, in particular to facilitate comparisons of the expression patterns of different genes and detection of their coexpression as a starting point for experimental studies. For this reason, we have included schematic illustrations of the gene expression in different stages of development when adequate information has been available. The site also contains a comprehensive list of references. Additionally phenotypic consequences of defective gene expression are indicated. The pages also provide links to other biological databases on the Internet, both as context-dependent and as general links. We welcome submissions from researches elsewhere to include their information of gene expression and function.

Animals↗

PubMed2003

From immunogenetics to immunomics: functional prospecting of genes and transcripts.

Human and mouse genome and transcriptome projects have expanded the field of 'immunogenetics' beyond the traditional study of the genetics and evolution of MHC, TCR and Ig loci into the new interdisciplinary area of 'immunomics'. Immunomics is the study of the molecular functions associated with all immune-related coding and non-coding mRNA transcripts. To unravel the function, regulation and diversity of the immunome requires that we identify and correctly categorize all immune-related transcripts. The importance of intercalated genes, antisense transcripts and non-coding RNAs and their potential role in regulation of immune development and function are only just starting to be appreciated. To better understand immune function and regulation, transcriptome projects (e.g. Functional Annotation of the Mouse, FANTOM), that focus on sequencing full-length transcripts from multiple tissue sources, ideally should include specific immune cells (e.g. T cell, B cells, macrophages, dendritic cells) at various states of development, in activated and unactivated states and in different disease contexts. Progress in deciphering immune regulatory networks will require the cooperative efforts of immunologists, immunogeneticists, molecular biologists and bioinformaticians. Although primary sequence analysis remains useful for annotation of new transcripts it is less useful for identifying novel functions of known transcripts in a new context (protein interaction network or pathway). The most efficient approach to mine useful information from the vast a priori knowledge contained in biological databases and the scientific literature, is to use a combination of computational and expert-driven knowledge discovery strategies. This paper will illustrate the challenges posed in attempts to functionally infer transcriptional regulation and interaction of immune-related genes from text and sequence-based data sources.

Alternative Splicing↗

PubMed1999

Transcription Regulatory Regions Database (TRRD):its status in 1999.

The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes. Release 4.1 of TRRD offers a number of significant improvements, in particular, a more detailed description of transcription factor binding sites, transcription factors per se, and gene expression patterns in a computer-readable format. In addition, the new TRRD release provides considerably more references to other molecular biological databases. TRRD 4.1 is installed under SRS and is available through the WWW at http://www.bionet.nsc.ru/trrd/

Animals↗

PubMed2004

The EF-Handome: combining comparative genomic study using FamDBtool, a new bioinformatics tool, and the network of expertise of the European Calcium Society.

By combining a bioinformatics tool (FamDBTool) and the expertise of a network of calcium binding proteins specialists (European Calcium Society), we aim to accelerate and to rationalize the curation of the public general biological database such as Swissprot and Entrez Gene with respect to specific protein families. In this paper, we show the feasibility of such rationale in order to set and to curate the human, mouse and rat sets of EF-Hand genes, the EF-Handome.

Animals↗

PubMed2003

Java editor for biological pathways.

SUMMARY: A visual Java-based tool for drawing and annotating biological pathways was developed. This tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. It is easy to use and system independent. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links.

Documentation↗

PubMed2004

Structure-chemical approach to organization of information on metabolic charts.

A nontraditional approach to construction of metabolic charts is proposed. It is based on the discovery of symmetry in the structure of the network of metabolic reactions. So if compounds and reactions are located on the metabolic chart according to their chemical features, the chart structure will acquire a periodic pattern. The charts thus created have a natural two-dimensional coordinate system of the metabolic network. Points on the X-axis correspond to number of carbon atoms in the carbon skeleton of compounds in columns and points on the Y-axis correspond to number of -COOH groups in compounds filing in series of rows on the charts. As a result this coordinate system sections the field of the charts into rectangular blocks each of which containing compounds with the same numbers of carbon atoms and the same numbers of -COOH groups. The latter substantially improves the charts and makes them a more valid source of metabolic data possessing heuristic properties. The periodicity of the metabolic network structure enables us easily to remember information about biochemical reactions and their products. The charts can also be used as a universal key for any biological database information that is systematically connected with the metabolic information. The charts can be important for medicine and pharmacology because they can help to understand the metabolic processes involved in decomposition of a particular drug or to find the chain of reactions blocked or initiated by administering this drug into a living organism.

Acids↗

PubMed2005

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs.

Single nucleotide polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. However, the accumulated sequence information on allelic variation is not matched by an understanding of the effect of SNPs on the functional attributes or 'molecular phenotype' of a protein. Towards this aim we developed SNPeffect, an online resource of human non-synonymous coding SNPs (nsSNPs) mapping phenotypic effects of allelic variation in human genes. SNPeffect contains 31 659 nsSNPs from 12 480 human proteins. The current release of SNPeffect incorporates data on protein stability, integrity of functional sites, protein phosphorylation and glycosylation, subcellular localization, protein turnover rates, protein aggregation, amyloidosis and chaperone interaction. The SNP entries are accessible through both a search and browse interface and are linked to most major biological databases. The data can be displayed as detailed descriptions of individual SNPs or as an overview of all SNPs for a given protein. SNPeffect will be regularly updated and can be accessed at http://snpeffect.vib.be/.

Alleles↗

PubMed2004

The major histocompatibility complex origin.

The present review focuses on the history of genes involved in the major histocompatibility complex (MHC), with a special emphasis on class I function in peptide presentation. The MHC class II story is covered in less detail, as it does not have a major impact on the general understanding of the MHC evolution. We first redefine the MHC as the definition evolved over time. We then use phylogenetic analysis to investigate the history of genes involved in the MHC class I process. As not all the genes involved in this process have been phylogenetically analyzed and because new sequences have been recently released in biological databases, we have re-investigated this matter. In the light of the phylogenetic analysis, the functions of the orthologs of the genes involved in MHC processes are examined in species not having an MHC system. We then demonstrate that the emergence of this new function is due to various levels of co-option.

Animals↗

PubMed2003

Will genomics revolutionise pharmaceutical R&D?

The successful identification of drug targets requires an understanding of the high-level functional interactions between the key components of cells, organs and systems, and how these interactions change in disease states. This information does not reside in the genome, or in the individual proteins that genes code for, it is to be found at a higher level. Genomics will succeed in revolutionising pharmaceutical research and development only if these interactions are also understood by determining the logic of healthy and diseased states. The rapid growth in biological databases, models of cells, tissues and organs, and in computing power has made it possible to explore functionality all the way from the level of genes to whole organs and systems. Combined with genomic and proteomic data, in silico simulation technology is set to transform all stages of drug discovery and development. The major obstacle to achieving this will be obtaining the relevant experimental data at levels higher than genomics and proteomics.

Cell Physiological Phenomena↗

PubMed2004

Exploring the diversity of complex metabolic networks.

MOTIVATION: Metabolism, the network of chemical reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochemical reaction from a given set of enzyme reaction rules that allows the de novo synthesis of metabolic pathways composed of these reactions, and the evaluation of these novel pathways with respect to their thermodynamic properties. RESULTS: We applied this framework to the analysis of the aromatic amino acid pathways and discovered almost 75,000 novel biochemical routes from chorismate to phenylalanine, more than 350,000 from chorismate to tyrosine, but only 13 from chorismate to tryptophan. Thermodynamic analysis of these pathways suggests that the native pathways are thermodynamically more favorable than the alternative possible pathways. The pathways generated involve compounds that exist in biological databases, as well as compounds that exist in chemical databases and novel compounds, suggesting novel biochemical routes for these compounds and the existence of biochemical compounds that remain to be discovered or synthesized through enzyme and pathway engineering. AVAILABILITY: Framework will be available via web interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). CONTACT: vassily@northwestern.edu or broadbelt@northwestern.edu SUPPLEMENTARY INFORMATION: http://systemsbiology.northwestern.edu/BNICE/publications.

Amino Acids, Aromatic↗

PubMed2005

The heart is already working.

Understanding the logic of living systems requires knowledge of the mechanisms involved at the levels at which functionality is expressed. This information resides neither in the genome, nor even in the individual proteins that genes code for. No functionality is expressed at these levels. It emerges as the result of interactions between many proteins relating to each other in multiple cascades and in interaction with the cellular environment. There is therefore no alternative to copying nature and computing these interactions to determine the logic of healthy and diseased states. The rapid growth in biological databases, models of cells, tissues and organs and the development of powerful computing hardware and algorithms have made it possible to explore functionality in a quantitative manner all the way from the level of genes to the physiological function of whole organs and regulatory systems. I use models of the heart to demonstrate that we can now go all the way from individual genetic information (on mutations, for example) to exploring the consequences at a whole-organ level.

Coronary Circulation↗

PubMed2005

Systems biology and the heart.

Understanding the logic of living systems requires knowledge of the mechanisms involved at the levels at which functionality is expressed. This information does not reside in the genome, nor even in the individual proteins that genes code for. No functionality is expressed at these levels. It emerges as the result of interactions between many proteins relating to each other in multiple cascades and in interaction with the cellular environment. There is, therefore, no alternative to copying nature and computing these interactions to determine the logic of healthy and diseased states. The rapid growth in biological databases, models of cells, tissues and organs and the development of powerful computing hardware and algorithms have made it possible to explore functionality in a quantitative manner all the way from the level of genes to the physiological function of whole organs and regulatory systems. I use models of the heart to demonstrate that we can now go all the way from individual genetic information (on mutations, for example) to exploring the consequences at a whole organ level.

Animals↗

PubMed2003

Classifying the precancers: a metadata approach.

BACKGROUND: During carcinogenesis, precancers are the morphologically identifiable lesions that precede invasive cancers. In theory, the successful treatment of precancers would result in the eradication of most human cancers. Despite the importance of these lesions, there has been no effort to list and classify all of the precancers. The purpose of this study is to describe the first comprehensive taxonomy and classification of the precancers. As a novel approach to disease classification, terms and classes were annotated with metadata (data that describes the data) so that the classification could be used to link precancer terms to data elements in other biological databases. METHODS: Terms in the UMLS (Unified Medical Language System) related to precancers were extracted. Extracted terms were reviewed and additional terms added. Each precancer was assigned one of six general classes. The entire classification was assembled as an XML (eXtensible Mark-up Language) file. A Perl script converted the XML file into a browser-viewable HTML (HyperText Mark-up Language) file. RESULTS: The classification contained 4700 precancer terms, 568 distinct precancer concepts and six precancer classes: 1) Acquired microscopic precancers; 2) acquired large lesions with microscopic atypia; 3) Precursor lesions occurring with inherited hyperplastic syndromes that progress to cancer; 4) Acquired diffuse hyperplasias and diffuse metaplasias; 5) Currently unclassified entities; and 6) Superclass and modifiers. CONCLUSION: This work represents the first attempt to create a comprehensive listing of the precancers, the first attempt to classify precancers by their biological properties and the first attempt to create a pathologic classification of precancers using standard metadata (XML). The classification is placed in the public domain, and comment is invited by the authors, who are prepared to curate and modify the classification.

Decision Support Systems, Clinical↗

PubMed2006

A Web-based assessment of bioinformatics end-user support services at US universities.

OBJECTIVES: This study was conducted to gauge the availability of bioinformatics end-user support services at US universities and to identify the providers of those services. The study primarily focused on the availability of short-term workshops that introduce users to molecular biology databases and analysis software. METHODS: Websites of selected US universities were reviewed to determine if bioinformatics educational workshops were offered, and, if so, what organizational units in the universities provided them. RESULTS: Of 239 reviewed universities, 72 (30%) offered bioinformatics educational workshops. These workshops were located at libraries (N = 15), bioinformatics centers (N = 38), or other facilities (N = 35). No such training was noted on the sites of 167 universities (70%). Of the 115 bioinformatics centers identified, two-thirds did not offer workshops. CONCLUSIONS: This analysis of university Websites indicates that a gap may exist in the availability of workshops and related training to assist researchers in the use of bioinformatics resources, representing a potential opportunity for libraries and other facilities to provide training and assistance for this growing user group.

Computational Biology↗

PubMed2000

Clozapine versus typical neuroleptic medication for schizophrenia.

BACKGROUND: Long-term drug treatment of schizophrenia with conventional antipsychotics has limitations: 25-33% of patients have illnesses that are treatment-resistant. Clozapine is an atypical antipsychotic drug, which is claimed to have superior efficacy and to cause fewer motor adverse effects than typical drugs for people with treatment-resistant illnesses. Clozapine carries a significant risk of serious blood disorders, which necessitates mandatory weekly blood monitoring at least during the first months of treatment. OBJECTIVES: To evaluate the effects of clozapine for schizophrenia in comparison to typical antipsychotic drugs. SEARCH STRATEGY: Publications in all languages were searched from the following databases: Biological Abstracts (1982-1999), The Cochrane Library CENTRAL (Issue 2, 1999), Cochrane Schizophrenia Group's Specialised Register (1999), EMbase (1980-1999), ISI Citation Index, LILACS (1982-1999), MEDLINE (1966-1999), and PsycLIT (1974-1999). Reference list screening of included papers was performed. Authors of recent trials and the manufacturer of clozapine contacted. SELECTION CRITERIA: All randomised controlled trials comparing clozapine with typical antipsychotic drugs were included by independent assessment by at least two reviewers. DATA COLLECTION AND ANALYSIS: Data were extracted independently by at least two reviewers. Authors of trials published since 1980 were contacted for additional and missing data. Odds ratios (OR) and 95% confidence intervals (CI) of homogeneous dichotomous data were calculated with the Peto method. A random effects model was used for heterogeneous dichotomous data. Where possible the numbers needed to treat (NNT) or needed to harm (NNH) were also calculated. Weighted or standardised means were calculated for continuous data. MAIN RESULTS: Currently the review includes 31 studies, 26 of which are less than 13 weeks in duration. These studies include 2589 participants, most of whom were men (74%). The average age was 38 years. There was no difference in the effects of clozapine and typical neuroleptic drugs for broad outcomes such as mortality, ability to work or suitability for discharge at end of the study. Clinical improvement was seen more frequently in those taking clozapine (random effects OR 0.4 CI 0.2-0.6, NNT 6) both in the short and the long term. Also, in the short term, participants on clozapine had fewer relapses than those on typical antipsychotic drugs (OR 0.6 CI 0.4-0.8, NNT 20 CI 17-38), and this may be true for long-term treatment as well. Symptom assessment scales showed a greater reduction of symptoms in clozapine-treated patients. Clozapine treatment was more acceptable than low-potency antipsychotics such as chlorpromazine (OR 0.6 CI 0.4-0.9) but did not differ from acceptability of high-potency neuroleptics such as haloperidol (random effects OR 0.8 CI 0.4-1.5). Clozapine was more acceptable in long-term treatment than conventional antipsychotic drugs (random effects OR 0.4 CI 0.2-0.7, NNT 6 CI 3-111). Patients were more satisfied with clozapine treatment (OR 0.5 CI 0.3-0.8, NNT 12 CI 7-37), but they experienced more hypersalivation, temperature increase, and drowsiness than those given conventional neuroleptics. However, clozapine patients experience fewer motor side effects and less dry mouth. The clinical efficacy of clozapine was more pronounced in participants resistant to typical neuroleptics in terms of clinical improvement (random effects OR 0.2 CI 0.1-0.5, NNT 5 CI 4-7) and symptom reduction. Thirty-two percent of treatment resistant people had a clinical improvement with clozapine treatment. REVIEWER'S CONCLUSIONS: This systematic review confirms that clozapine is convincingly more effective than typical antipsychotic drugs in reducing symptoms of schizophrenia, producing clinically meaningful improvements and postponing relapse. Patients were more satisfied with clozapine treatment than with typical neuroleptic treatment. (ABSTRACT TRUNCATED

Antipsychotic Agents↗

PubMed2000

Newer atypical antipsychotic medication versus clozapine for schizophrenia.

BACKGROUND: Clozapine is an atypical antipsychotic drug, which is claimed to have superior efficacy and to cause fewer movement disorders. However, clozapine carries a significant risk of serious blood disorders. Newer atypical antipsychotics are safer alternatives that might share the benefits of clozapine. It is thus of interest to compare the effectiveness of newer atypical antipsychotics with the effectiveness of clozapine. OBJECTIVES: To evaluate the clinical effects of newer atypical antipsychotic drugs in comparison to clozapine for schizophrenia. SEARCH STRATEGY: Publications in all languages were searched from the following databases: Biological Abstracts/BIOSIS (1980-1999), The Cochrane Schizophrenia Group's Register of Trials (1998), The Cochrane Library CENTRAL Register (Issue 4, 1999), EMBASE (1980-1998), MEDLINE (1966-1999), LILACS/CD-ROM (1998), and PsycLIT/PsycINFO (1974-1999). Trials were also sought from recent conference proceedings and reference lists of included papers. Authors of recent trials and the manufacturers of clozapine, iloperidone, olanzapine, quetiapine, remoxipride, risperidone, sertindole, ziprasidone and zotepine were contacted. SELECTION CRITERIA: All randomised controlled trials comparing clozapine with newer atypical antipsychotic drugs were included by independent assessment by two reviewers. DATA COLLECTION AND ANALYSIS: Data were extracted independently by two reviewers. Relative risks (RR) and 95% confidence intervals (CI) of homogenous dichotomous data were calculated. A random effects model was used for heterogeneous dichotomous data. Where possible the number needed to treat (NNT) statistic with 95%CI were also calculated. Weighted or standardised means were calculated for continuous data. Due to the small number of included studies, sensitivity analyses or funnel plot statistics were not undertaken for this version of the review. MAIN RESULTS: The current review includes eight studies (22 papers), of which three studies are 4-6 weeks in duration and only one study is of more than 12 weeks' duration. Newer atypical drugs seemed to be broadly similar to clozapine using a clinical global index or trialists' definitions of improvement, but this result was obtained from a relatively small number of studies. Due to the small number of studies and patients, wide confidence intervals were seen when their effectiveness as measured by symptom rating scales was compared. Social functioning was better in patients on newer atypical medication (risperidone) than in those on clozapine, but this finding is based on a single underpowered trial and has to be interpreted with caution. Clozapine and newer atypical drugs showed their adverse effect profile to be dissimilar: while clozapine produced more fatigue, hypersalivation, nausea, and orthostatic dizziness, new atypical drugs, with the exception of olanzapine, produced more extrapyramidal symptoms. The impact of these drugs and their effects on patients' day-to-day quality of life, service use, hospital admission, and pharmacoeconomics was not measured. REVIEWER'S CONCLUSIONS: The equal effectiveness and tolerability of new atypical drugs in comparison with clozapine is not yet demonstrated. Lack of statistical power to determine the comparative efficacy and effectiveness of newer atypical drugs makes it difficult to judge whether newer drugs are more effective, less effective or equivalent. Trials of sufficient power, with longer duration, measuring clinically important outcomes, are needed to assess the true comparative clinical effectiveness, tolerability and cost effectiveness of newer drugs in relation to clozapine.

Antipsychotic Agents↗

PubMed2000

Polyunsaturated fatty acid (fish or evening primrose oil) for schizophrenia.

BACKGROUND: Limited evidence gives support to an hypothesis suggesting that the symptoms of schizophrenia may result from altered neuronal membrane structure and metabolism. The latter are dependent on blood plasma levels of certain essential fatty acids (EFAs) and their metabolites. Several studies have shown those with schizophrenia often have low levels of the particular EFAs necessary for normal nerve cell membrane metabolism. OBJECTIVES: To review the effects of supplementing standard antipsychotic treatment with polyunsaturated fatty acids, whether essential (EFAs) or non-essential, for those with schizophrenia and, in recent updates to also evaluate the effects of EFA's as a sole antipsychotic treatment. To evaluate the relative efficacy of different types of fatty acid supplementation. SEARCH STRATEGY: Relevant randomised trials were identified by searching the following electronic databases: Biological Abstracts (1985-1998), CINAHL (1982-1998), Cochrane Library (Issue 4, 1999), Cochrane Schizophrenia Group's Register (February 2000), EMBASE (1980-1998), MEDLINE (1966-1998) and PsycLIT (1974-1998). In addition, reviewers searched references of included and excluded studies and contacted authors to identify further studies. SELECTION CRITERIA: All randomised clinical trials of polyunsaturated fatty acid supplementation to standard treatment or as primary intervention for schizophrenia (however defined) versus standard care. DATA COLLECTION AND ANALYSIS: Reviewers evaluated data independently and analysed on an intention-to-treat basis. They assumed that people who left the study early or were lost to follow-up had no improvement. Where possible and appropriate relative risk (RR) and their 95% confidence intervals (CI) were calculated. The number needed to treat (NNT) was estimated. For continuous data weighted mean differences (WMD) and their 95% confidence intervals were calculated. Data were inspected for heterogeneity and publication biases. MAIN RESULTS: Four relatively small trials (total n=204) showed low levels of loss to follow up and adverse effects for those taking essential fatty acids. Early results from a few trials suggest a positive effect of eicosapentaenoic acid (EPA) over placebo for scale-derived mental state outcomes. The data, however, is limited making these results difficult to analyse and interpret with confidence. A single small study (n=30) investigated the value of using EPA as sole treatment for people hospitalised for relapse. Results suggest that EPA may help one third of people avoid instigation of standard antipsychotic drugs for 12 weeks (RR 0.6, CI 0.4-0.91). There were no clear effects of primrose oil (omega-6) EFA supplementation. REVIEWER'S CONCLUSIONS: All data are preliminary, but results look encouraging for fish oil. EPA does not seem harmful, may be acceptable to people with schizophrenia and have moderately positive effect. A further trial is soon to be reported from the USA and more are underway or planned in the South Africa and Norway. Considering that EPA may be an acceptable intervention, large, long simple studies reporting clincially meaningful data should be anticipated.

Antipsychotic Agents↗